/*
 *                  BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 * 
 * Created on May 21, 2006
 *
 */
package pl.com.like.sequoia.biojava.pdb.align;

import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;

import org.biojava.bio.structure.Atom;
import org.biojava.bio.structure.AtomImpl;
import org.biojava.bio.structure.Calc;
import org.biojava.bio.structure.SVDSuperimposer;
import org.biojava.bio.structure.Structure;
import org.biojava.bio.structure.StructureException;
import org.biojava.bio.structure.StructureTools;
import org.biojava.bio.structure.align.StrucAligParameters;
import org.biojava.bio.structure.align.helper.AlignTools;
import org.biojava.bio.structure.align.helper.JointFragments;
import org.biojava.bio.structure.align.pairwise.AltAligComparator;
import org.biojava.bio.structure.align.pairwise.AlternativeAlignment;
import org.biojava.bio.structure.align.pairwise.FragmentJoiner;
import org.biojava.bio.structure.align.pairwise.FragmentPair;
import org.biojava.bio.structure.gui.BiojavaJmol;
import org.biojava.bio.structure.io.PDBFileParser;
import org.biojava.bio.structure.jama.Matrix;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * Perform a pairwise protein structure superimposition.
 * 
 * <p>
 * The algorithm is a distance matrix based, rigid body protein structure superimposition. It is based on a variation of
 * the PSC++ algorithm provided by Peter Lackner (Peter.Lackner@sbg.ac.at, personal communication) .
 * </p>
 * 
 * 
 * 
 * <h2>Example</h2>
 * 
 * <pre>
 *  public void run(){
 * 
 * 		// first load two example structures
 * 		{@link InputStream} inStream1 = this.getClass().getResourceAsStream("/files/5pti.pdb");        
 * 		{@link InputStream} inStream2 = this.getClass().getResourceAsStream("/files/1tap.pdb");
 * 
 * 		{@link Structure} structure1 = null;
 * 		{@link Structure} structure2 = null;
 * 
 * 		{@link PDBFileParser} pdbpars = new {@link PDBFileParser}();
 * 		try {
 * 			structure1 = pdbpars.parsePDBFile(inStream1) ;
 * 			structure2 = pdbpars.parsePDBFile(inStream2);
 * 
 * 		} catch ({@link IOException} e) {
 * 			e.printStackTrace();
 * 			return;
 * 		}
 * 
 * 		// calculate structure superimposition for two complete structures
 * 		{@link StructurePairAligner} aligner = new {@link StructurePairAligner}();
 * 
 * 
 * 		try {
 * 			// align the full 2 structures with default parameters.
 * 			// see StructurePairAligner for more options and how to align
 * 			// any set of Atoms
 * 			aligner.align(structure1,structure2);
 * 
 * 			{@link AlternativeAlignment}[] aligs = aligner.getAlignments();
 * 			{@link AlternativeAlignment} a = aligs[0];          
 * 			System.out.println(a);
 * 
 * 			//display the alignment in Jmol
 * 
 * 			// first get an artificial structure for the alignment
 * 			{@link Structure} artificial = a.getAlignedStructure(structure1, structure2);
 * 
 * 
 * 			// and then send it to Jmol (only will work if Jmol is in the Classpath) 
 * 
 * 			{@link BiojavaJmol} jmol = new {@link BiojavaJmol}();
 * 			jmol.setTitle(artificial.getName());
 * 			jmol.setStructure(artificial);
 * 
 * 			// color the two structures
 * 
 * 
 * 			jmol.evalString("select *; backbone 0.4; wireframe off; spacefill off; " + 
 * 					"select not protein and not solvent; spacefill on;");
 * 			jmol.evalString("select *"+"/1 ; color red; model 1; ");
 * 
 * 
 * 			// now color the equivalent residues ...
 * 
 * 			String[] pdb1 = a.getPDBresnum1();
 * 			for (String res : pdb1 ){		
 * 				jmol.evalString("select " + res + "/1 ; backbone 0.6; color white;");
 * 			}
 * 
 * 			jmol.evalString("select *"+"/2; color blue; model 2;");
 * 			String[] pdb2 = a.getPDBresnum2();
 * 			for (String res :pdb2 ){
 * 				jmol.evalString("select " + res + "/2 ; backbone 0.6; color yellow;");
 * 			}
 * 
 * 
 * 			// now show both models again.
 * 			jmol.evalString("model 0;");
 * 
 * 		} catch ({@link StructureException} e){
 * 			e.printStackTrace();
 * 		}
 * 	}
 * </pre>
 * 
 * 
 * 
 * @author Andreas Prlic
 * @author Peter Lackner
 * @since 1.4
 * @version %I% %G%
 */
public class StructurePairAligner {

	public static final Logger log = LoggerFactory.getLogger(StructurePairAligner.class);

	/**
	 * example usage of this class
	 * 
	 * @param args
	 */
	// public static void main(String[] args) {
	// try {
	//
	// // UPDATE THE FOLLOWING LINES TO MATCH YOUR SETUP
	//
	// PDBFileReader pdbr = new PDBFileReader();
	// pdbr.setPath("/Users/andreas/WORK/PDB/");
	//
	// // String pdb1 = "1crl";
	// // String pdb2 = "1ede";
	//
	// String pdb1 = "1buz";
	// String pdb2 = "1ali";
	// String outputfile = "/tmp/alig_" + pdb1 + "_" + pdb2 + ".pdb";
	//
	// // NO NEED TO DO CHANGE ANYTHING BELOW HERE...
	//
	// StructurePairAligner sc = new StructurePairAligner();
	//
	// // step1 : read molecules
	//
	// System.out.println("aligning " + pdb1 + " vs. " + pdb2);
	//
	// Structure s1 = pdbr.getStructureById(pdb1);
	// Structure s2 = pdbr.getStructureById(pdb2);
	//
	// // step 2 : do the calculations
	// sc.align(s1, s2);
	//
	// AlternativeAlignment[] aligs = sc.getAlignments();
	//
	// // cluster similar results together
	// ClusterAltAligs.cluster(aligs);
	//
	// // print the result:
	// // the AlternativeAlignment object gives also access to rotation matrices / shift vectors.
	// for (AlternativeAlignment aa : aligs) {
	// System.out.println(aa);
	// }
	//
	// // convert AlternativeAlignemnt 1 to PDB file, so it can be opened with a viewer (e.g. Jmol, Rasmol)
	//
	// if (aligs.length > 0) {
	// AlternativeAlignment aa1 = aligs[0];
	// String pdbstr = aa1.toPDB(s1, s2);
	//
	// System.out.println("writing alignment to " + outputfile);
	// FileOutputStream out = new FileOutputStream(outputfile);
	// PrintStream p = new PrintStream(out);
	//
	// p.println(pdbstr);
	//
	// p.close();
	// out.close();
	// }
	//
	// // display the alignment in Jmol
	// // only will work if Jmol is in the Classpath
	//
	// if (aligs.length > 0) {
	//
	// if (!BiojavaJmol.jmolInClassPath()) {
	// System.err.println("Could not find Jmol in classpath, please install first!");
	// return;
	// }
	//
	// AlternativeAlignment aa1 = aligs[0];
	//
	// // first get an artificial structure for the alignment
	// Structure artificial = aa1.getAlignedStructure(s1, s2);
	//
	// // and then send it to Jmol (only will work if Jmol is in the Classpath)
	// BiojavaJmol jmol = new BiojavaJmol();
	// jmol.setTitle(artificial.getName());
	// jmol.setStructure(artificial);
	//
	// // color the two structures
	//
	// jmol.evalString("select *; backbone 0.4; wireframe off; spacefill off; "
	// + "select not protein and not solvent; spacefill on;");
	// jmol.evalString("select */1 ; color red; model 1; ");
	//
	// // now color the equivalent residues ...
	//
	// String[] pdbs1 = aa1.getPDBresnum1();
	// for (String res : pdbs1) {
	// jmol.evalString("select " + res + "/1 ; backbone 0.6; color white;");
	// }
	//
	// jmol.evalString("select */2; color blue; model 2;");
	// String[] pdbs2 = aa1.getPDBresnum2();
	// for (String res : pdbs2) {
	// jmol.evalString("select " + res + "/2 ; backbone 0.6; color yellow;");
	// }
	//
	// // now show both models again.
	// jmol.evalString("model 0;");
	//
	// jmol.evalString("echo done.");
	// }
	//
	// } catch (Exception e) {
	// e.printStackTrace();
	// }
	//
	// }

	AlternativeAlignment[] alts;
	Matrix distanceMatrix;
	StrucAligParameters params;

	FragmentPair[] fragPairs;

	boolean debug = false;

	public StructurePairAligner() {
		super();
		params = StrucAligParameters.getDefaultParameters();
		reset();
		alts = new AlternativeAlignment[0];
		distanceMatrix = new Matrix(0, 0);
	}

	/**
	 * calculate the protein structure superimposition, between two sets of atoms.
	 * 
	 * 
	 * 
	 * @param ca1 set of Atoms of structure 1
	 * @param ca2 set of Atoms of structure 2
	 * @param params the parameters to use for the alignment
	 * @throws StructureException
	 */
	public void align(Atom[] ca1, Atom[] ca2, StrucAligParameters params) throws StructureException {

		reset();

		// step 1 get all Diagonals of length X that are similar between both structures
		if (debug) {
			System.out.println(" length atoms1:" + ca1.length);
			System.out.println(" length atoms2:" + ca2.length);

			System.out.println("step 1 - get fragments with similar intramolecular distances ");
		}
		int k = params.getDiagonalDistance();
		int k2 = params.getDiagonalDistance2();
		int fragmentLength = params.getFragmentLength();

		if (ca1.length < (fragmentLength + 1) || ca2.length < (fragmentLength + 1)) {
			throw new StructureException("structure too short, can not align");
		}
		int rows = ca1.length - fragmentLength + 1;
		int cols = ca2.length - fragmentLength + 1;
		// System.out.println("rows " + rows + " " + cols +
		// " ca1 l " + ca1.length + " ca2 l " + ca2.length);
		distanceMatrix = new Matrix(rows, cols, 0.0);

		double[] dist1 = AlignTools.getDiagonalAtK(ca1, k);

		double[] dist2 = AlignTools.getDiagonalAtK(ca2, k);
		double[] dist3 = new double[0];
		double[] dist4 = new double[0];
		if (k2 > 0) {
			dist3 = AlignTools.getDiagonalAtK(ca1, k2);
			dist4 = AlignTools.getDiagonalAtK(ca2, k2);
		}

		double[][] utmp = new double[][] { { 0, 0, 1 } };
		// Matrix unitv = new Matrix(utmp);
		Atom unitvector = new AtomImpl();
		unitvector.setCoords(utmp[0]);

		List<FragmentPair> fragments = new ArrayList<FragmentPair>();

		for (int i = 0; i < rows; i++) {

			Atom[] catmp1 = AlignTools.getFragment(ca1, i, fragmentLength);
			Atom center1 = AlignTools.getCenter(ca1, i, fragmentLength);

			for (int j = 0; j < cols; j++) {

				double rdd1 = AlignTools.rms_dk_diag(dist1, dist2, i, j, fragmentLength, k);
				double rdd2 = 0;
				if (k2 > 0) {
					rdd2 = AlignTools.rms_dk_diag(dist3, dist4, i, j, fragmentLength, k2);
				}
				double rdd = rdd1 + rdd2;
				distanceMatrix.set(i, j, rdd);

				if (rdd < params.getFragmentMiniDistance()) {
					FragmentPair f = new FragmentPair(fragmentLength, i, j);
					// System.out.println("i " + i + " " + j );
					try {

						Atom[] catmp2 = AlignTools.getFragment(ca2, j, fragmentLength);
						Atom center2 = AlignTools.getCenter(ca2, j, fragmentLength);

						// System.out.println("c1 : " + center1 + " c2: " + center2);
						f.setCenter1(center1);
						f.setCenter2(center2);

						SVDSuperimposer svd = new SVDSuperimposer(catmp1, catmp2);
						Matrix rotmat = svd.getRotation();
						// rotmat.print(3,3);
						f.setRot(rotmat);

						Atom aunitv = (Atom) unitvector.clone();
						Calc.rotate(aunitv, rotmat);
						f.setUnitv(aunitv);

						boolean doNotAdd = false;
						if (params.reduceInitialFragments()) {
							doNotAdd = FragmentJoiner.reduceFragments(fragments, f, distanceMatrix);

						}
						if (doNotAdd) {
							continue;
						}

						fragments.add(f);

					} catch (StructureException e) {
						e.printStackTrace();
						break;
					}
				}
			}
		}

		FragmentPair[] fp = fragments.toArray(new FragmentPair[fragments.size()]);
		setFragmentPairs(fp);

		if (debug) {
			System.out.println(" got # fragment pairs: " + fp.length);
		}

		if (debug) {
			System.out.println("step 2 - join fragments");
		}

		// step 2 combine them to possible models
		FragmentJoiner joiner = new FragmentJoiner();

		JointFragments[] frags;

		if (!params.isJoinPlo()) {
			frags = joiner.approach_ap3(ca1, ca2, fp, params);
		} else {

			// this approach by StrComPy (peter lackner):
			frags = joiner.frag_pairwise_compat(fp, params.getAngleDiff(), params.getFragCompat(), params
					.getMaxrefine());
		}

		if (debug) {
			System.out.println(" number joint fragments:" + frags.length);
		}

		if (debug) {
			System.out.println("step 3 - refine alignments");
		}

		List<AlternativeAlignment> aas = new ArrayList<AlternativeAlignment>();
		for (int i = 0; i < frags.length; i++) {
			JointFragments f = frags[i];
			AlternativeAlignment a = new AlternativeAlignment();
			// System.out.println(f.getRms());
			// a.setRms(f.getRms());
			a.apairs_from_idxlst(f);
			a.setAltAligNumber(i + 1);
			a.setDistanceMatrix(distanceMatrix);

			try {
				if (params.getMaxIter() > 0) {

					a.refine(params, ca1, ca2);
				} else {
					a.finish(params, ca1, ca2);

				}
			} catch (StructureException e) {
				e.printStackTrace();
			}
			a.calcScores(ca1, ca2);
			// a.getRotationMatrix().print(3,3);
			aas.add(a);
		}

		// sort the alternative alignments
		Comparator<AlternativeAlignment> comp = new AltAligComparator();
		Collections.sort(aas, comp);
		Collections.reverse(aas);

		alts = aas.toArray(new AlternativeAlignment[aas.size()]);
		// do final numbering of alternative solutions
		int aanbr = 0;
		for (AlternativeAlignment a : alts) {
			aanbr++;
			a.setAltAligNumber(aanbr);
			// System.out.println(aanbr);
			// a.getRotationMatrix().print(3,3);
		}
		// System.out.println("calc done");
	}

	/**
	 * calculate the alignment between the two full structures with default parameters
	 * 
	 * @param s1
	 * @param s2
	 * @throws StructureException
	 */
	public void align(Structure s1, Structure s2) throws StructureException {

		align(s1, s2, params);
	}

	/**
	 * calculate the alignment between the two full structures with user provided parameters
	 * 
	 * @param s1
	 * @param s2
	 * @param params
	 * @throws StructureException
	 */
	public void align(Structure s1, Structure s2, StrucAligParameters params) throws StructureException {
		// step 1 convert the structures to Atom Arrays

		Atom[] ca1 = getAlignmentAtoms(s1);
		Atom[] ca2 = getAlignmentAtoms(s2);

		align(ca1, ca2, params);
	}

	public Atom[] getAlignmentAtoms(Structure s) {
		String[] atomNames = params.getUsedAtomNames();
		return StructureTools.getAtomArray(s, atomNames);
	}

	/**
	 * return the alternative alignments that can be found for the two structures
	 * 
	 * @return AlternativeAlignment[] array
	 */
	public AlternativeAlignment[] getAlignments() {
		return alts;
	}

	/**
	 * return the difference of distance matrix between the two structures
	 * 
	 * @return a Matrix
	 */
	public Matrix getDistMat() {
		return distanceMatrix;
	}

	/**
	 * get the results of step 1 - the FragmentPairs used for seeding the alignment
	 * 
	 * @return a FragmentPair[] array
	 */

	public FragmentPair[] getFragmentPairs() {
		return fragPairs;
	}

	/**
	 * get the parameters.
	 * 
	 * @return the Parameters.
	 */
	public StrucAligParameters getParams() {
		return params;
	}

	/**
	 * check if debug mode is set on
	 * 
	 * @return debug flag
	 */
	public boolean isDebug() {
		return debug;
	}

	private void reset() {
		alts = new AlternativeAlignment[0];
		distanceMatrix = new Matrix(0, 0);
		fragPairs = new FragmentPair[0];

	}

	/**
	 * set the debug flag
	 * 
	 * @param debug flag
	 */
	public void setDebug(boolean debug) {
		this.debug = debug;
	}

	public void setFragmentPairs(FragmentPair[] fragPairs) {
		this.fragPairs = fragPairs;
	}

	/**
	 * set the parameters to be used for the algorithm
	 * 
	 * @param params the Parameter object
	 */
	public void setParams(StrucAligParameters params) {
		this.params = params;
	}

}
